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diff vcfcheck.xml @ 4:2b86cb8d0d51 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 12:54:30 +0000
parents 713575be4f77
children 8628527d2d7f
line wrap: on
line diff
--- a/vcfcheck.xml	Mon Mar 26 12:12:34 2018 -0400
+++ b/vcfcheck.xml	Thu Jan 23 12:54:30 2020 +0000
@@ -7,14 +7,15 @@
     <stdio>
         <regex match="index file" source="stderr" level="warning"/>
     </stdio>
-    <command>
+    <command><![CDATA[
         #set $reference_fasta_filename = "localref.fa"
         #if str( $reference_source.reference_source_selector ) == "history":
-            ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+            ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
         #else:
             #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
         #end if
-        vcfcheck $failure_selector -f "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
+        vcfcheck $failure_selector -f '${reference_fasta_filename}' '${input_vcf}' > '${out_file1}'
+    ]]></command>
     <inputs>
         <conditional name="reference_source">
             <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">